[gmx-users] TOPOLOGY-FILE:how to add topology for a new residue
Mr.Sridhar
sridhar at www.cdfd.org.in
Fri Apr 25 11:03:00 CEST 2003
This is the topology file for PHORBOL-13-ACETATE that I got from PRODRG
#########################################################################
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0
;#include "ffgmx.itp"
;#include "spc.itp"
[ moleculetype ]
;name nrexcl
PRB 3
;
[ atoms ]
; nr type resnr resid atom cgnr charge
1 CH3 1 PRB CA2 1 0.000
2 C 1 PRB CA1 2 0.000
3 OM 1 PRB OA2 3 0.000
4 OS 1 PRB OA1 4 0.000
5 CB 1 PRB C13 5 0.000
6 CB 1 PRB C15 6 0.000
7 CH3 1 PRB C16 7 0.000
8 CH3 1 PRB C17 8 0.000
9 CH1 1 PRB C14 9 0.000
10 CH1 1 PRB C8 10 0.000
11 CR61 1 PRB C7 11 0.000
12 CB 1 PRB C6 12 0.000
13 CH2 1 PRB C20 13 0.150
14 OA 1 PRB O20 13 -0.548
15 HO 1 PRB HAD 13 0.398
16 CH2 1 PRB C5 14 0.000
17 CB 1 PRB C4 15 0.150
18 OA 1 PRB O4 15 -0.548
19 HO 1 PRB HAA 15 0.398
20 CB 1 PRB C3 16 0.380
21 O 1 PRB O3 16 -0.380
22 CB 1 PRB C2 17 0.000
23 CH3 1 PRB C19 18 0.000
24 CR51 1 PRB C1 19 0.000
25 CH1 1 PRB C10 20 0.000
26 CB 1 PRB C9 21 0.150
27 OA 1 PRB O9 21 -0.548
28 HO 1 PRB HAB 21 0.398
29 CH1 1 PRB C11 22 0.000
30 CH3 1 PRB C18 23 0.000
31 CH1 1 PRB C12 24 0.150
32 OA 1 PRB O12 24 -0.548
33 HO 1 PRB HAC 24 0.398
[ bonds ]
;ai aj fu c0 c1
1 2 1 0.153 3347200.0 0.153 3347200.0 ; CA2 CA1
2 3 1 0.125 4184000.0 0.125 4184000.0 ; CA1 OA2
2 4 1 0.136 3765600.0 0.136 3765600.0 ; CA1 OA1
4 5 1 0.143 2510400.0 0.143 2510400.0 ; OA1 C13
5 6 1 0.139 4184000.0 0.139 4184000.0 ; C13 C15
5 9 1 0.153 3347200.0 0.153 3347200.0 ; C13 C14
5 31 1 0.153 3347200.0 0.153 3347200.0 ; C13 C12
6 7 1 0.153 3347200.0 0.153 3347200.0 ; C15 C16
6 8 1 0.153 3347200.0 0.153 3347200.0 ; C15 C17
6 9 1 0.153 3347200.0 0.153 3347200.0 ; C15 C14
9 10 1 0.153 3347200.0 0.153 3347200.0 ; C14 C8
10 11 1 0.153 3347200.0 0.153 3347200.0 ; C8 C7
10 26 1 0.153 3347200.0 0.153 3347200.0 ; C8 C9
11 12 1 0.139 4184000.0 0.139 4184000.0 ; C7 C6
12 13 1 0.153 3347200.0 0.153 3347200.0 ; C6 C20
12 16 1 0.153 3347200.0 0.153 3347200.0 ; C6 C5
13 14 1 0.143 3347200.0 0.143 3347200.0 ; C20 O20
14 15 1 0.100 3138000.0 0.100 3138000.0 ; O20 HAD
16 17 1 0.153 3347200.0 0.153 3347200.0 ; C5 C4
17 18 1 0.136 3765600.0 0.136 3765600.0 ; C4 O4
17 20 1 0.139 4184000.0 0.139 4184000.0 ; C4 C3
17 25 1 0.153 3347200.0 0.153 3347200.0 ; C4 C10
18 19 1 0.100 3138000.0 0.100 3138000.0 ; O4 HAA
20 21 1 0.123 5020800.0 0.123 5020800.0 ; C3 O3
20 22 1 0.139 4184000.0 0.139 4184000.0 ; C3 C2
22 23 1 0.153 3347200.0 0.153 3347200.0 ; C2 C19
22 24 1 0.133 4184000.0 0.133 4184000.0 ; C2 C1
24 25 1 0.153 3347200.0 0.153 3347200.0 ; C1 C10
25 26 1 0.153 3347200.0 0.153 3347200.0 ; C10 C9
26 27 1 0.136 3765600.0 0.136 3765600.0 ; C9 O9
26 29 1 0.153 3347200.0 0.153 3347200.0 ; C9 C11
27 28 1 0.100 3138000.0 0.100 3138000.0 ; O9 HAB
29 30 1 0.153 3347200.0 0.153 3347200.0 ; C11 C18
29 31 1 0.153 3347200.0 0.153 3347200.0 ; C11 C12
31 32 1 0.143 3347200.0 0.143 3347200.0 ; C12 O12
32 33 1 0.100 3138000.0 0.100 3138000.0 ; O12 HAC
[ pairs ]
;ai aj fu c0 c1
1 5 1 ; CA2 CA1
2 6 1 ; CA1 OA2
2 9 1 ; CA1 OA2
2 31 1 ; CA1 OA2
3 5 1 ; CA1 OA1
4 6 1 ; OA1 C13
4 7 1 ; OA1 C13
4 8 1 ; OA1 C13
4 9 1 ; OA1 C13
4 10 1 ; OA1 C13
4 29 1 ; OA1 C13
4 32 1 ; OA1 C13
5 7 1 ; C13 C15
5 8 1 ; C13 C15
5 10 1 ; C13 C15
5 11 1 ; C13 C15
5 26 1 ; C13 C15
5 30 1 ; C13 C15
5 33 1 ; C13 C15
6 10 1 ; C13 C14
6 11 1 ; C13 C14
6 26 1 ; C13 C14
6 29 1 ; C13 C14
6 31 1 ; C13 C14
6 32 1 ; C13 C14
7 9 1 ; C13 C12
7 10 1 ; C13 C12
7 31 1 ; C13 C12
8 9 1 ; C15 C16
8 10 1 ; C15 C16
8 31 1 ; C15 C16
9 12 1 ; C15 C17
9 25 1 ; C15 C17
9 27 1 ; C15 C17
9 29 1 ; C15 C17
9 31 1 ; C15 C17
9 32 1 ; C15 C17
10 13 1 ; C15 C14
10 16 1 ; C15 C14
10 17 1 ; C15 C14
10 24 1 ; C15 C14
10 28 1 ; C15 C14
10 30 1 ; C15 C14
10 31 1 ; C15 C14
11 14 1 ; C14 C8
11 17 1 ; C14 C8
11 25 1 ; C14 C8
11 27 1 ; C14 C8
11 29 1 ; C14 C8
12 15 1 ; C8 C7
12 18 1 ; C8 C7
12 20 1 ; C8 C7
12 25 1 ; C8 C7
12 26 1 ; C8 C7
13 17 1 ; C8 C9
14 16 1 ; C7 C6
16 19 1 ; C6 C5
16 21 1 ; C6 C5
16 22 1 ; C6 C5
16 24 1 ; C6 C5
16 26 1 ; C6 C5
17 22 1 ; C20 O20
17 23 1 ; C20 O20
17 24 1 ; C20 O20
17 27 1 ; C20 O20
17 29 1 ; C20 O20
18 21 1 ; O20 HAD
18 22 1 ; O20 HAD
18 24 1 ; O20 HAD
18 26 1 ; O20 HAD
19 20 1 ; C5 C4
19 25 1 ; C5 C4
20 24 1 ; C4 O4
20 25 1 ; C4 O4
20 26 1 ; C4 O4
21 23 1 ; C4 C3
21 24 1 ; C4 C3
21 25 1 ; C4 C3
22 25 1 ; C4 C10
22 26 1 ; C4 C10
23 25 1 ; O4 HAA
24 27 1 ; C3 O3
24 29 1 ; C3 O3
25 28 1 ; C3 C2
25 30 1 ; C3 C2
25 31 1 ; C3 C2
26 32 1 ; C2 C19
27 30 1 ; C2 C1
27 31 1 ; C2 C1
28 29 1 ; C1 C10
29 33 1 ; C10 C9
30 32 1 ; C9 O9
[ angles ]
;ai aj ak fu c0 c1
1 2 3 1 120.0 418.4 120.0 418.4 ; CA2 CA1 OA2
1 2 4 1 120.0 418.4 120.0 418.4 ; CA2 CA1 OA1
3 2 4 1 120.0 418.4 120.0 418.4 ; OA2 CA1 OA1
2 4 5 1 109.5 334.7 109.5 334.7 ; CA1 OA1 C13
4 5 6 1 115.0 502.1 115.0 502.1 ; OA1 C13 C15
4 5 9 1 115.0 502.1 115.0 502.1 ; OA1 C13 C14
6 5 9 1 60.0 418.4 60.0 418.4 ; C15 C13 C14
4 5 31 1 109.5 460.2 109.5 460.2 ; OA1 C13 C12
6 5 31 1 115.0 502.1 115.0 502.1 ; C15 C13 C12
9 5 31 1 115.0 502.1 115.0 502.1 ; C14 C13 C12
5 6 7 1 115.0 502.1 115.0 502.1 ; C13 C15 C16
5 6 8 1 115.0 502.1 115.0 502.1 ; C13 C15 C17
7 6 8 1 109.5 460.2 109.5 460.2 ; C16 C15 C17
5 6 9 1 60.0 418.4 60.0 418.4 ; C13 C15 C14
7 6 9 1 115.0 502.1 115.0 502.1 ; C16 C15 C14
8 6 9 1 115.0 502.1 115.0 502.1 ; C17 C15 C14
5 9 6 1 60.0 418.4 60.0 418.4 ; C13 C14 C15
5 9 10 1 115.0 502.1 115.0 502.1 ; C13 C14 C8
6 9 10 1 115.0 502.1 115.0 502.1 ; C15 C14 C8
9 10 11 1 109.5 460.2 109.5 460.2 ; C14 C8 C7
9 10 26 1 111.0 460.2 111.0 460.2 ; C14 C8 C9
11 10 26 1 109.5 460.2 109.5 460.2 ; C7 C8 C9
10 11 12 1 120.0 418.4 120.0 418.4 ; C8 C7 C6
11 12 13 1 120.0 418.4 120.0 418.4 ; C7 C6 C20
11 12 16 1 120.0 418.4 120.0 418.4 ; C7 C6 C5
13 12 16 1 120.0 418.4 120.0 418.4 ; C20 C6 C5
12 13 14 1 111.0 460.2 111.0 460.2 ; C6 C20 O20
13 14 15 1 109.5 397.5 109.5 397.5 ; C20 O20 HAD
12 16 17 1 111.0 460.2 111.0 460.2 ; C6 C5 C4
16 17 18 1 109.5 460.2 109.5 460.2 ; C5 C4 O4
16 17 20 1 126.0 418.4 126.0 418.4 ; C5 C4 C3
18 17 20 1 109.5 460.2 109.5 460.2 ; O4 C4 C3
16 17 25 1 109.5 460.2 109.5 460.2 ; C5 C4 C10
18 17 25 1 109.5 460.2 109.5 460.2 ; O4 C4 C10
20 17 25 1 104.0 460.2 104.0 460.2 ; C3 C4 C10
17 18 19 1 109.5 397.5 109.5 397.5 ; C4 O4 HAA
17 20 21 1 120.0 418.4 120.0 418.4 ; C4 C3 O3
17 20 22 1 120.0 418.4 120.0 418.4 ; C4 C3 C2
21 20 22 1 120.0 418.4 120.0 418.4 ; O3 C3 C2
20 22 23 1 120.0 418.4 120.0 418.4 ; C3 C2 C19
20 22 24 1 108.0 418.4 108.0 418.4 ; C3 C2 C1
23 22 24 1 120.0 418.4 120.0 418.4 ; C19 C2 C1
22 24 25 1 120.0 418.4 120.0 418.4 ; C2 C1 C10
17 25 24 1 104.0 460.2 104.0 460.2 ; C4 C10 C1
17 25 26 1 111.0 460.2 111.0 460.2 ; C4 C10 C9
24 25 26 1 109.5 460.2 109.5 460.2 ; C1 C10 C9
10 26 25 1 109.5 460.2 109.5 460.2 ; C8 C9 C10
10 26 27 1 109.5 460.2 109.5 460.2 ; C8 C9 O9
25 26 27 1 109.5 460.2 109.5 460.2 ; C10 C9 O9
10 26 29 1 109.5 460.2 109.5 460.2 ; C8 C9 C11
25 26 29 1 109.5 460.2 109.5 460.2 ; C10 C9 C11
27 26 29 1 109.5 460.2 109.5 460.2 ; O9 C9 C11
26 27 28 1 109.5 397.5 109.5 397.5 ; C9 O9 HAB
26 29 30 1 111.0 460.2 111.0 460.2 ; C9 C11 C18
26 29 31 1 111.0 460.2 111.0 460.2 ; C9 C11 C12
30 29 31 1 111.0 460.2 111.0 460.2 ; C18 C11 C12
5 31 29 1 111.0 460.2 111.0 460.2 ; C13 C12 C11
5 31 32 1 109.5 460.2 109.5 460.2 ; C13 C12 O12
29 31 32 1 109.5 460.2 109.5 460.2 ; C11 C12 O12
31 32 33 1 109.5 397.5 109.5 397.5 ; C12 O12 HAC
[ dihedrals ]
;ai aj ak al fu c0 c1 m c0 c1 m
2 1 4 3 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI CA1 CA2 OA1
OA2
12 13 16 11 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C6 C20 C5
C7
20 21 17 22 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C3 O3 C4
C2
22 24 23 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C2 C1 C19
C3
5 4 6 9 2 58.5 836.8 0 58.5 836.8 0 ; IDI C13 OA1 C15
C14
6 7 5 9 2 58.5 836.8 0 58.5 836.8 0 ; IDI C15 C16 C13
C14
9 10 6 5 2 58.5 836.8 0 58.5 836.8 0 ; IDI C14 C8 C15
C13
10 9 11 26 2 35.3 836.8 0 35.3 836.8 0 ; IDI C8 C14 C7
C9
17 16 18 20 2 35.3 836.8 0 35.3 836.8 0 ; IDI C4 C5 O4
C3
25 17 26 24 2 35.3 836.8 0 35.3 836.8 0 ; IDI C10 C4 C9
C1
26 10 25 27 2 35.3 836.8 0 35.3 836.8 0 ; IDI C9 C8 C10
O9
29 26 30 31 2 35.3 836.8 0 35.3 836.8 0 ; IDI C11 C9 C18
C12
31 5 32 29 2 35.3 836.8 0 35.3 836.8 0 ; IDI C12 C13 O12
C11
1 2 4 5 1 180.0 16.7 2 180.0 16.7 2 ; DI CA2 CA1 OA1
C13
31 5 4 2 1 0.0 3.8 6 0.0 3.8 6 ; DI C12 C13 OA1
CA1
4 5 31 32 1 0.0 5.9 3 0.0 5.9 3 ; DI OA1 C13 C12
O12
26 10 9 5 1 0.0 5.9 3 0.0 5.9 3 ; DI C9 C8 C14
C13
9 10 11 12 1 0.0 0.4 6 0.0 0.4 6 ; DI C14 C8 C7
C6
9 10 26 29 1 0.0 5.9 3 0.0 5.9 3 ; DI C14 C8 C9
C11
16 12 11 10 1 180.0 41.8 2 180.0 41.8 2 ; DI C5 C6 C7
C8
11 12 13 14 1 0.0 0.4 6 0.0 0.4 6 ; DI C7 C6 C20
O20
11 12 16 17 1 0.0 0.4 6 0.0 0.4 6 ; DI C7 C6 C5
C4
12 13 14 15 1 0.0 1.3 3 0.0 1.3 3 ; DI C6 C20 O20
HAD
25 17 16 12 1 0.0 0.4 6 0.0 0.4 6 ; DI C10 C4 C5
C6
16 17 18 19 1 180.0 7.1 2 180.0 7.1 2 ; DI C5 C4 O4
HAA
16 17 20 22 1 0.0 0.4 6 0.0 0.4 6 ; DI C5 C4 C3
C2
16 17 25 26 1 0.0 5.9 3 0.0 5.9 3 ; DI C5 C4 C10
C9
17 20 22 24 1 180.0 5.9 2 180.0 5.9 2 ; DI C4 C3 C2
C1
20 22 24 25 1 180.0 5.9 2 180.0 5.9 2 ; DI C3 C2 C1
C10
22 24 25 26 1 0.0 0.4 6 0.0 0.4 6 ; DI C2 C1 C10
C9
17 25 26 29 1 0.0 5.9 3 0.0 5.9 3 ; DI C4 C10 C9
C11
10 26 27 28 1 180.0 7.1 2 180.0 7.1 2 ; DI C8 C9 O9
HAB
10 26 29 31 1 0.0 5.9 3 0.0 5.9 3 ; DI C8 C9 C11
C12
32 31 29 26 1 0.0 5.9 3 0.0 5.9 3 ; DI O12 C12 C11
C9
5 31 32 33 1 0.0 1.3 3 0.0 1.3 3 ; DI C13 C12 O12
HAC
;[ system ]
;PROPRB
[ molecules ]
PRB 1
More information about the gromacs.org_gmx-users
mailing list